Works by Tegnér, Jesper

Results: 69

Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3.

Published in:

BMC Biology, 2018, v. 16, n. 1, p. 1, doi. 10.1186/s12915-018-0518-3

By:

Schmidt, Angelika;
Marabita, Francesco;
Kiani, Narsis A.;
Gross, Catharina C.;
Johansson, Henrik J.;
Éliás, Szabolcs;
Rautio, Sini;
Eriksson, Matilda;
Fernandes, Sunjay Jude;
Silberberg, Gilad;
Ullah, Ubaid;
Bhatia, Urvashi;
Lähdesmäki, Harri;
Lehtiö, Janne;
Gomez-Cabrero, David;
Wiendl, Heinz;
Lahesmaa, Riitta;
Tegnér, Jesper

Publication type:

Article

DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2722, doi. 10.1093/bioinformatics/btab147

By:

Liu-Wei, Wang;
Kafkas, Şenay;
Chen, Jun;
Dimonaco, Nicholas J.;
Tegnér, Jesper;
Hoehndorf, Robert

Publication type:

Article

Pre-B cell to macrophage transdifferentiation without significant promoter DNA methylation changes.

Published in:

Nucleic Acids Research, 2012, v. 40, n. 5, p. 1954

By:

Rodríguez-Ubreva, Javier;
Ciudad, Laura;
Gómez-Cabrero, David;
Parra, Maribel;
Bussmann, Lars H.;
di Tullio, Alessandro;
Kallin, Eric M.;
Tegnér, Jesper;
Graf, Thomas;
Ballestar, Esteban

Publication type:

Article

Laboratory biomarkers and frailty: presentation of the FRAILOMIC initiative.

Published in:

Clinical Chemistry & Laboratory Medicine, 2015, v. 53, n. 10, p. e253, doi. 10.1515/cclm-2015-0147

By:

Lippi, Giuseppe;
Jansen-Duerr, Pidder;
Viña, Jose;
Durrance-Bagale, Anna;
Abugessaisa, Imad;
Gomez-Cabrero, David;
Tegnér, Jesper;
Grillari, Johannes;
Erusalimsky, Jorge;
Sinclair, Alan;
Rodriguez-Manãs, Leocadio

Publication type:

Article

Approximations of algorithmic and structural complexity validate cognitive-behavioral experimental results.

Published in:

Frontiers in Computational Neuroscience, 2023, v. 16, p. 1, doi. 10.3389/fncom.2022.956074

By:

Zenil, Hector;
Marshall, James A. R.;
Tegnér, Jesper

Publication type:

Article

Transcriptional Profiling Uncovers a Network of Cholesterol-Responsive Atherosclerosis Target Genes.

Published in:

PLoS Genetics, 2008, v. 4, n. 3, p. 1, doi. 10.1371/journal.pgen.1000036

By:

Skogsberg, Josefin;
Lundström, Jesper;
Kovacs, Alexander;
Nilsson, Roland;
Noori, Peri;
Maleki, Shohreh;
Köhler, Marina;
Hamsten, Anders;
Tegnér, Jesper;
Björkegren, Johan

Publication type:

Article

Dynamics and heterogeneity of brain damage in multiple sclerosis.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 10, p. 1, doi. 10.1371/journal.pcbi.1005757

By:

Kotelnikova, Ekaterina;
Kiani, Narsis A.;
Abad, Elena;
Martinez-Lapiscina, Elena H.;
Andorra, Magi;
Zubizarreta, Irati;
Pulido-Valdeolivas, Irene;
Pertsovskaya, Inna;
Alexopoulos, Leonidas G.;
Olsson, Tomas;
Martin, Roland;
Paul, Friedemann;
Tegnér, Jesper;
Garcia-Ojalvo, Jordi;
Villoslada, Pablo

Publication type:

Article

Deep neural network prediction of genome-wide transcriptome signatures – beyond the Black-box.

Published in:

NPJ Systems Biology & Applications, 2022, v. 8, n. 1, p. 1, doi. 10.1038/s41540-022-00218-9

By:

Magnusson, Rasmus;
Tegnér, Jesper N.;
Gustafsson, Mika

Publication type:

Article

Human macrophages induce CD4+Foxp3+ regulatory T cells via binding and re-release of TGF-β.

Published in:

Immunology & Cell Biology, 2016, v. 94, n. 8, p. 747, doi. 10.1038/icb.2016.34

By:

Schmidt, Angelika;
Zhang, Xing‐Mei;
Joshi, Rubin N;
Iqbal, Shasina;
Wahlund, Casper;
Gabrielsson, Susanne;
Harris, Robert A;
Tegnér, Jesper

Publication type:

Article

Comparative Analysis of Protocols to Induce Human CD4+Foxp3+ Regulatory T Cells by Combinations of IL-2, TGF-beta, Retinoic Acid, Rapamycin and Butyrate.

Published in:

PLoS ONE, 2016, v. 11, n. 2, p. 1, doi. 10.1371/journal.pone.0148474

By:

Schmidt, Angelika;
Eriksson, Matilda;
Shang, Ming-Mei;
Weyd, Heiko;
Tegnér, Jesper

Publication type:

Article

Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders.

Published in:

International Journal of Molecular Sciences, 2015, v. 16, n. 12, p. 29179, doi. 10.3390/ijms161226148

By:

Hofmann-Apitius, Martin;
Ball, Gordon;
Gebel, Stephan;
Bagewadi, Shweta;
Bono, Bernard de;
Schneider, Reinhard;
Page, Matt;
Kodamullil, Alpha Tom;
Younesi, Erfan;
Ebeling, Christian;
Tegnér, Jesper;
Canard, Luc

Publication type:

Article

Normalization of circulating microRNA expression data obtained by quantitative real-time RT-PCR.

Published in:

Briefings in Bioinformatics, 2016, v. 17, n. 2, p. 204, doi. 10.1093/bib/bbv056

By:

Marabita, Francesco;
Candia, Paola de;
Torri, Anna;
Tegnér, Jesper;
Abrignani, Sergio;
Rossi, Riccardo L.

Publication type:

Article

The dynamical stability of reverberatory neural circuits.

Published in:

Biological Cybernetics, 2002, v. 87, n. 5/6, p. 471, doi. 10.1007/s00422-002-0363-9

By:

Tegnér, Jesper;
Compte, Albert;
Wang, Xiao-Jing

Publication type:

Article

Challenges in the Multivariate Analysis of Mass Cytometry Data: The Effect of Randomization.

Published in:

Cytometry. Part A, 2019, v. 95, n. 11, p. 1178, doi. 10.1002/cyto.a.23908

By:

Papoutsoglou, Georgios;
Lagani, Vincenzo;
Schmidt, Angelika;
Tsirlis, Konstantinos;
Cabrero, David‐Gómez;
Tegnér, Jesper;
Tsamardinos, Ioannis

Publication type:

Article

Phosphatase inhibitor PPP1R11 modulates resistance of human T cells toward Treg‐mediated suppression of cytokine expression.

Published in:

Journal of Leukocyte Biology, 2019, v. 106, n. 2, p. 413, doi. 10.1002/JLB.2A0618-228R

By:

Joshi, Rubin N.;
Fernandes, Sunjay Jude;
Shang, Ming‐Mei;
Kiani, Narsis A.;
Gomez‐Cabrero, David;
Tegnér, Jesper;
Schmidt, Angelika

Publication type:

Article

HiDi: an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation.

Published in:

Bioinformatics, 2017, v. 33, n. 24, p. 3964, doi. 10.1093/bioinformatics/btx501

By:

Yue Deng;
Zenil, Hector;
Tegnér, Jesper;
Kiani, Narsis A.

Publication type:

Article

Exhaustion of CD4+ T-cells mediated by the Kynurenine Pathway in Melanoma.

Published in:

Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-48635-x

By:

Rad Pour, Soudabeh;
Morikawa, Hiromasa;
Kiani, Narsis A.;
Yang, Muyi;
Azimi, Alireza;
Shafi, Gowhar;
Shang, Mingmei;
Baumgartner, Roland;
Ketelhuth, Daniel F. J.;
Kamleh, Muhammad Anas;
Wheelock, Craig E.;
Lundqvist, Andreas;
Hansson, Johan;
Tegnér, Jesper

Publication type:

Article

Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients.

Published in:

Scientific Reports, 2019, v. 9, n. 1, p. 1, doi. 10.1038/s41598-019-48493-7

By:

Fernandes, Sunjay Jude;
Morikawa, Hiromasa;
Ewing, Ewoud;
Ruhrmann, Sabrina;
Joshi, Rubin Narayan;
Lagani, Vincenzo;
Karathanasis, Nestoras;
Khademi, Mohsen;
Planell, Nuria;
Schmidt, Angelika;
Tsamardinos, Ioannis;
Olsson, Tomas;
Piehl, Fredrik;
Kockum, Ingrid;
Jagodic, Maja;
Tegnér, Jesper;
Gomez-Cabrero, David

Publication type:

Article

Immunometabolic Network Interactions of the Kynurenine Pathway in Cutaneous Malignant Melanoma.

Published in:

Frontiers in Oncology, 2020, v. 10, p. 1, doi. 10.3389/fonc.2020.00051

By:

Rad Pour, Soudabeh;
Morikawa, Hiromasa;
Kiani, Narsis A.;
Gomez-Cabrero, David;
Hayes, Alistair;
Zheng, Xiaozhong;
Pernemalm, Maria;
Lehtiö, Janne;
Mole, Damian J.;
Hansson, Johan;
Eriksson, Hanna;
Tegnér, Jesper

Publication type:

Article

Neuronal firing rates account for distractor effects on mnemonic accuracy in a visuo-spatial working memory task.

Published in:

Biological Cybernetics, 2007, v. 96, n. 4, p. 407, doi. 10.1007/s00422-006-0139-8

By:

Macoveanu, Julian;
Klingberg, Torkel;
Tegnér, Jesper

Publication type:

Article

Data integration in the era of omics: current and future challenges.

Published in:

BMC Systems Biology, 2014, v. 8, n. Suppl 2, p. 1, doi. 10.1186/1752-0509-8-S2-I1

By:

Gomez-Cabrero, David;
Abugessaisa, Imad;
Maier, Dieter;
Teschendorff, Andrew;
Merkenschlager, Matthias;
Gisel, Andreas;
Ballestar, Esteban;
Bongcam-Rudloff, Erik;
Conesa, Ana;
Tegnér, Jesper

Publication type:

Article

Computational disease modeling - fact or fiction?

Published in:

BMC Systems Biology, 2009, v. 3, p. 1, doi. 10.1186/1752-0509-3-56

By:

Tegnér, Jesper N.;
Compte, Albert;
Auffray, Charles;
An, Gary;
Cedersund, Gunnar;
Clermont, Gilles;
Gutkin, Boris;
Oltvai, Zoltán N.;
Stephan, Klaas Enno;
Thomas, Randy;
Villoslada, Pablo

Publication type:

Article

From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration.

Published in:

BMC Bioinformatics, 2016, v. 17, p. 23, doi. 10.1186/s12859-016-1291-3

By:

Gomez-Cabrero, David;
Menche, Jörg;
Vargas, Claudia;
Cano, Isaac;
Maier, Dieter;
Barabási, Albert-László;
Tegnér, Jesper;
Roca, Josep

Publication type:

Article

Brain Activity Related to Working Memory and Distraction in Children and Adults.

Published in:

Cerebral Cortex, 2007, v. 17, n. 5, p. 1047

By:

Olesen, Pernille J.;
Macoveanu, Julian;
Tegnér, Jesper;
Klingberg, Torkel

Publication type:

Article

Monozygotic twins discordant for common variable immunodeficiency reveal impaired DNA demethylation during naïve-to-memory B-cell transition.

Published in:

Nature Communications, 2015, v. 6, n. 6, p. 7335, doi. 10.1038/ncomms8335

By:

Rodríguez-Cortez, Virginia C.;
del Pino-Molina, Lucia;
Rodríguez-Ubreva, Javier;
Ciudad, Laura;
Gómez-Cabrero, David;
Company, Carlos;
Urquiza, José M.;
Tegnér, Jesper;
Rodríguez-Gallego, Carlos;
López-Granados, Eduardo;
Ballestar, Esteban

Publication type:

Article

Non-HLA genes PTPN22, CDK6 and PADI4 are associated with specific autoantibodies in HLA-defined subgroups of rheumatoid arthritis.

Published in:

Arthritis Research & Therapy, 2014, v. 16, n. 5, p. 2, doi. 10.1186/s13075-014-0414-3

By:

Snir, Omri;
Gomez-Cabrero, David;
Montes, Ariana;
Perez-Pampin, Eva;
Gómez-Reino, Juan J.;
Seddighzadeh, Maria;
Klich, Katharina U.;
Israelsson, Lena;
Ding, Bo;
Catrina, Anca I.;
Holmdahl, Rikard;
Alfredsson, Lars;
Klareskog, Lars;
Tegnér, Jesper;
Gonzalez, Antonio;
Malmström, Vivianne;
Padyukov, Leonid

Publication type:

Article

The Thermodynamics of Network Coding, and an Algorithmic Refinement of the Principle of Maximum Entropy †.

Published in:

Entropy, 2019, v. 21, n. 6, p. 560, doi. 10.3390/e21060560

By:

Zenil, Hector;
Kiani, Narsis A.;
Tegnér, Jesper

Publication type:

Article

A Decomposition Method for Global Evaluation of Shannon Entropy and Local Estimations of Algorithmic Complexity.

Published in:

Entropy, 2018, v. 20, n. 8, p. 605, doi. 10.3390/e20080605

By:

Zenil, Hector;
Hernández-Orozco, Santiago;
Kiani, Narsis A.;
Soler-Toscano, Fernando;
Rueda-Toicen, Antonio;
Tegnér, Jesper

Publication type:

Article

A Review of Graph and Network Complexity from an Algorithmic Information Perspective.

Published in:

Entropy, 2018, v. 20, n. 8, p. 551, doi. 10.3390/e20080551

By:

Zenil, Hector;
Kiani, Narsis A.;
Tegnér, Jesper

Publication type:

Article

Symmetry and Correspondence of Algorithmic Complexity over Geometric, Spatial and Topological Representations †.

Published in:

Entropy, 2018, v. 20, n. 7, p. 534, doi. 10.3390/e20070534

By:

Zenil, Hector;
Kiani, Narsis A.;
Tegnér, Jesper

Publication type:

Article

On reliable discovery of molecular signatures.

Published in:

BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-38

By:

Nilsson, Roland;
Björkegren, Johan;
Tegnér, Jesper

Publication type:

Article

Electrotonic Signals along Intracellular Membranes May Interconnect Dendritic Spines and Nucleus.

Published in:

PLoS Computational Biology, 2008, v. 4, n. 3, p. 1, doi. 10.1371/journal.pcbi.1000036

By:

Shemer, Isaac;
Brinne, Björn;
Tegnér, Jesper;
Grillner, Sten

Publication type:

Article

Reverse Engineering of Gene Networks with LASSO and Nonlinear Basis Functions.

Published in:

Annals of the New York Academy of Sciences, 2009, v. 1158, p. 265, doi. 10.1111/j.1749-6632.2008.03764.x

By:

Gustafsson, Mika;
Hörnquist, Michael;
Lundström, Jesper;
Björkegren, Johan;
Tegnér, Jesper

Publication type:

Article

FRONTO-PARIETAL CONNECTION ASYMMETRY REGULATES WORKING MEMORY DISTRACTIBILITY.

Published in:

Journal of Integrative Neuroscience, 2007, v. 6, n. 4, p. 567, doi. 10.1142/S0219635207001702

By:

EDIN, FREDRIK;
KLINGBERG, TORKEL;
STÖDBERG, TOMMY;
TEGNÉR, JESPER

Publication type:

Article

Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells.

Published in:

2021

By:

Éliás, Szabolcs;
Schmidt, Angelika;
Gomez-Cabrero, David;
Tegnér, Jesper

Publication type:

journal article

Quantifying loss of information in network-based dimensionality reduction techniques.

Published in:

Journal of Complex Networks, 2016, v. 4, n. 3, p. 342, doi. 10.1093/comnet/cnv025

By:

ZENIL, HECTOR;
KIANI, NARSIS A.;
TEGNÉR, JESPER

Publication type:

Article

SCENERY: a web application for (causal) network reconstruction from cytometry data.

Published in:

Nucleic Acids Research, 2017, v. 45, n. W1, p. W270, doi. 10.1093/nar/gkx448

By:

Papoutsoglou, Georgios;
Athineou, Giorgos;
Lagani, Vincenzo;
Xanthopoulos, Iordanis;
Schmidt, Angelika;
Éliás, Szabolcs;
Tegnér, Jesper;
Tsamardinos, Ioannis

Publication type:

Article

High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis.

Published in:

Genome Medicine, 2016, v. 8, p. 1, doi. 10.1186/s13073-016-0374-0

By:

Gomez-Cabrero, David;
Almgren, Malin;
Sjöholm, Louise K.;
Hensvold, Aase H.;
Ringh, Mikael V.;
Tryggvadottir, Rakel;
Kere, Juha;
Scheynius, Annika;
Acevedo, Nathalie;
Reinius, Lovisa;
Taub, Margaret A.;
Montano, Carolina;
Aryee, Martin J.;
Feinberg, Jason I.;
Feinberg, Andrew P.;
Tegnér, Jesper;
Klareskog, Lars;
Catrina, Anca I.;
Ekström, Tomas J.

Publication type:

Article

Endurance training changes the DNA methylation pattern in human skeletal muscle.

Published in:

FASEB Journal, 2013, v. 27, p. 1134.1, doi. 10.1096/fasebj.27.1_supplement.1134.1

By:

Lindholm, Malene Elin;
Marabita, Francesco;
Gomez‐Cabrero, David;
Fischer, Heléne;
Tegnér, Jesper;
Sundberg, Carl Johan

Publication type:

Article

Stronger Synaptic Connectivity as a Mechanism behind Development of Working Memory--related Brain Activity during Childhood.

Published in:

Journal of Cognitive Neuroscience, 2007, v. 19, n. 5, p. 750, doi. 10.1162/jocn.2007.19.5.750

By:

Edin, Fredrik;
Macoveanu, Julian;
Olesen, Pernille;
Tegnér, Jesper;
Klingberg, Torkel

Publication type:

Article

An Algorithm for Reading Dependencies from the Minimal Undirected Independence Map of a Graphoid that Satisfies Weak Transitivity.

Published in:

Journal of Machine Learning Research, 2009, v. 10, n. 5, p. 1071

By:

Peña, Jose M.;
Nilsson, Roland;
Björkegren, Johan;
Tegnér, Jesper

Publication type:

Article

Consistent Feature Selection for Pattern Recognition in Polynomial Time.

Published in:

Journal of Machine Learning Research, 2007, v. 8, n. 3, p. 589

By:

Nilson, Roland;
Peña, José M.;
Bjökegren, Johan;
Tegnér, Jesper

Publication type:

Article

Phosphoproteomics reveals regulatory T cell-Mediated DeF6 Dephosphorylation That affects cytokine expression in human conventional T cells.

Published in:

Frontiers in Immunology, 2017, p. 1, doi. 10.3389/fimmu.2017.01163

By:

Joshi, Rubin N.;
Binai, Nadine A.;
Marabita, Francesco;
Zhenhua Sui;
Altman, Amnon;
Heck, Albert J. R.;
Tegnér, Jesper;
Schmidt, Angelika

Publication type:

Article

TGF-β Affects the Differentiation of Human GM-CSF+ CD4+ T Cells in an Activation- and Sodium-Dependent Manner.

Published in:

Frontiers in Immunology, 2016, v. 7, p. 1, doi. 10.3389/fimmu.2016.00603

By:

Éliás, Szabolcs;
Schmidt, Angelika;
Kannan, Venkateshan;
Andersson, John;
Tegnér, Jesper

Publication type:

Article

Harmonization of quality metrics and power calculation in multi-omic studies.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-16937-8

By:

Tarazona, Sonia;
Balzano-Nogueira, Leandro;
Gómez-Cabrero, David;
Schmidt, Andreas;
Imhof, Axel;
Hankemeier, Thomas;
Tegnér, Jesper;
Westerhuis, Johan A.;
Conesa, Ana

Publication type:

Article

Harmonization of quality metrics and power calculation in multi-omic studies.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-16937-8

By:

Tarazona, Sonia;
Balzano-Nogueira, Leandro;
Gómez-Cabrero, David;
Schmidt, Andreas;
Imhof, Axel;
Hankemeier, Thomas;
Tegnér, Jesper;
Westerhuis, Johan A.;
Conesa, Ana

Publication type:

Article

ParkDB: a Parkinson’s disease gene expression database.

Published in:

Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 7, p. 1

By:

Taccioli, Cristian;
Maselli, Vincenza;
Tegnér, Jesper;
Gomez-Cabrero, David;
Altobelli, Gioia;
Emmett, Warren;
Lescai, Francesco;
Gustincich, Stefano;
Stupka, Elia

Publication type:

Article

ParkDB: a Parkinson’s disease gene expression database.

Published in:

Database: The Journal of Biological Databases & Curation, 2011, v. 2011, n. 7, p. 1

By:

Taccioli, Cristian;
Tegnér, Jesper;
Maselli, Vincenza;
Gomez-Cabrero, David;
Altobelli, Gioia;
Emmett, Warren;
Lescai, Francesco;
Gustincich, Stefano;
Stupka, Elia

Publication type:

Article

Oxygen Pathway Modeling Estimates High Reactive Oxygen Species Production above the Highest Permanent Human Habitation.

Published in:

PLoS ONE, 2014, v. 9, n. 11, p. 1, doi. 10.1371/journal.pone.0111068

By:

Cano, Isaac;
Selivanov, Vitaly;
Gomez-Cabrero, David;
Tegnér, Jesper;
Roca, Josep;
Wagner, Peter D.;
Cascante, Marta

Publication type:

Article

Accelerating Translational Research by Clinically Driven Development of an Informatics Platform–A Case Study.

Published in:

PLoS ONE, 2014, v. 9, n. 9, p. 1, doi. 10.1371/journal.pone.0104382

By:

Abugessaisa, Imad;
Saevarsdottir, Saedis;
Tsipras, Giorgos;
Lindblad, Staffan;
Sandin, Charlotta;
Nikamo, Pernilla;
Ståhle, Mona;
Malmström, Vivianne;
Klareskog, Lars;
Tegnér, Jesper

Publication type:

Article